About this course

This course will explore computational techniques for processing and
analyzing large-scale biological sequence coming from the genomics
revolution. We will study string search and comparison algorithms, data
structures for efficiently storing and querying strings, and techniques
such as Hidden Markov Models for finding patterns within long strings. The
emphasis will be on the underlying algorithms, rather than on the use of
particular tools or databases (though examples of widely used tool will be
presented).

Instructor:Carl
Kingsford; carlk AT cs.umd.edu; Office hours: by appointment in CBCB
3113.
Stephen
Altschul (NIH) will give a significant number of the lectures.

Class Time: MWF, 10:00-10:50.

Prerequisites: No previous biological knowledge is required. A
certain amount of mathematical maturity is required (that any CS Ph.D.
student will likely have) and basic familiarity with algorithm design
techniques will be assumed. The class will generally be self-contained.

Grading: There will be several homework sets, a midterm, an
in-class final, and a class programming project.

Credit: This course is a core Ph.D. or M.S. course, and it
does count towards MS Comps. The area is Bioinformatics.

HAMILTON: Steinman won half of the Nobel Prize. The other half went to two
scientists who figured out a more basic part of the immune system, known as
innate immunity. One of them is Jules Hoffmann, who ran a research laboratory
at the University of Strasbourg in France until a couple of years ago. In 1996,
Hoffmann discovered a gene in fruit flies that helps them fend off fungal and
bacterial infections. The other scientist is Bruce Beutler, from Scripps
Research Institute in California. In 1998, Beutler showed that fruit flies and
mammals use a similar system to trigger an immune response. Beutler says he
made the discovery one night after five frustrating years of research.

Dr. BRUCE BEUTLER: I was in my study looking over the results of BLAST analysis
- those are sequence comparisons - and I saw the mutation that we were after,
and I was absolutely thrilled. I was just shaking.